Pass through 'resolver' when loading workflow steps. (#498)

* Pass through 'resolver' when loading workflow steps.

* Don't try to update entries that are not in pathmap.

* Use self.realpath() so subclasses work as expected.

Author: tetron

cwltool/draft2tool.py

@@ -220,7 +220,7 @@ def makePathMapper(self, reffiles, stagedir, **kwargs):
 
     def updatePathmap(self, outdir, pathmap, fn):
         # type: (Text, PathMapper, Dict) -> None
-        if "location" in fn:
+        if "location" in fn and fn["location"] in pathmap:
             pathmap.update(fn["location"], pathmap.mapper(fn["location"]).resolved,
                            os.path.join(outdir, fn["basename"]),
                            ("Writable" if fn.get("writable") else "") + fn["class"], False)

cwltool/pathmapper.py

@@ -252,3 +252,6 @@ def reversemap(self, target):  # type: (Text) -> Tuple[Text, Text]
 
     def update(self, key, resolved, target, type, stage):  # type: (Text, Text, Text, Text, bool) -> None
         self._pathmap[key] = MapperEnt(resolved, target, type, stage)
+
+    def __contains__(self, key):
+        return key in self._pathmap

cwltool/stdfsaccess.py

@@ -67,4 +67,4 @@ def docker_compatible_realpath(self, path):  # type: (Text) -> Text
             if path.startswith('/'):
                 return path
             return '/'+path
-        return os.path.realpath(path)
+        return self.realpath(path)

cwltool/workflow.py

@@ -673,7 +673,8 @@ def __init__(self, toolpath_object, pos, **kwargs):
                     toolpath_object["run"], kwargs.get("makeTool"), kwargs,
                     enable_dev=kwargs.get("enable_dev"),
                     strict=kwargs.get("strict"),
-                    fetcher_constructor=kwargs.get("fetcher_constructor"))
+                    fetcher_constructor=kwargs.get("fetcher_constructor"),
+                    resolver=kwargs.get("resolver"))
         except validate.ValidationException as v:
             raise WorkflowException(
                 u"Tool definition %s failed validation:\n%s" %